6.1 years ago by
There's no robust way that I'm aware of. As dariober hinted at, there are too many caveats to consider when comparing peaks across two very different technologies. However, depending on your ultimate objective, you could perform an ad hoc analysis that could tell you a few things. You could use bedtools or the IRanges capabilities of R to tell you how well the peaks overlap between the two experiments - that's the most basic level of differential analysis. You could then use those same tools to define the common regions called as peaks between both platforms, and compare the distributions of scores (i.e. each might be a ratio over background) under the common areas to see how comparable they are. To quantify differences you might have to normalize them to each other, or transform them to a similar scale (i.e. z-score, etc.), or examine them by rank - a lot depends on what the data looks like, and what you're really trying to get out of it.